data_DL5
# 
_chem_comp.id                                    DL5 
_chem_comp.name                                  
;Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H18 N8 O18 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         TNP-AMPPCP 
_chem_comp.pdbx_formal_charge                    -1 
_chem_comp.pdbx_initial_date                     2015-06-03 
_chem_comp.pdbx_modified_date                    2026-04-05 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        715.289 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DL5 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        5A3R 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              ? 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
DL5 N1     N1     N 0  1 Y N N N N N 1.198  0.881 14.137 -4.051 5.905  1.020  N1     DL5 1  
DL5 C2     C2     C 0  1 Y N N N N N 2.497  1.233 13.845 -4.180 4.761  1.668  C2     DL5 2  
DL5 N3     N3     N 0  1 Y N N N N N 2.836  2.538 13.563 -3.470 3.694  1.366  N3     DL5 3  
DL5 C4     C4     C 0  1 Y N N N N N 1.923  3.602 13.547 -2.581 3.730  0.379  C4     DL5 4  
DL5 C5     C5     C 0  1 Y N N N N N 0.597  3.280 13.838 -2.406 4.923  -0.341 C5     DL5 5  
DL5 C6     C6     C 0  1 Y N N N N N 0.212  1.921 14.136 -3.187 6.035  0.018  C6     DL5 6  
DL5 N6     N6     N 0  1 N N N N N N -1.078 1.640 14.418 -3.060 7.237  -0.655 N6     DL5 7  
DL5 N7     N7     N 0  1 Y N N N N N -0.172 4.373 13.791 -1.455 4.690  -1.277 N7     DL5 8  
DL5 C8     C8     C 0  1 Y N N N N N 0.650  5.328 13.483 -1.044 3.459  -1.179 C8     DL5 9  
DL5 N9     N9     N 0  1 Y N N N N N 1.946  4.952 13.312 -1.708 2.825  -0.172 N9     DL5 10 
DL5 PA     PA     P 0  1 N N N N N N -0.582 7.780 10.265 3.452  -1.417 -0.949 PA     DL5 11 
DL5 PB     PB     P 0  1 N N N N N N -2.967 6.552 11.742 6.249  -0.730 -0.250 PB     DL5 12 
DL5 PG     PG     P 0  1 N N N N N N -4.064 3.716 11.801 8.810  0.101  1.021  PG     DL5 13 
DL5 C01    C01    C 0  1 N N N N N N -3.261 5.029 12.670 7.018  -0.111 1.283  C01    DL5 14 
DL5 "C1'"  "C1'"  C 0  1 N N R N N N 3.186  5.732 12.958 -1.524 1.433  0.246  "C1'"  DL5 15 
DL5 O1A    O1A    O 0  1 N N N N N N 0.209  7.500 8.922  3.622  -0.874 -2.316 O1A    DL5 16 
DL5 O1B    O1B    O 0  1 N N N N N N -2.660 7.591 12.659 6.905  -2.147 -0.645 O1B    DL5 17 
DL5 C1F    C1F    C 0  1 N N N N N N 5.739  6.408 10.760 -3.699 -1.293 0.224  C1F    DL5 18 
DL5 O1G    O1G    O 0  1 N N N N N N -5.010 4.211 10.608 9.413  -1.201 0.658  O1G    DL5 19 
DL5 "C2'"  "C2'"  C 0  1 N N R N N N 3.644  5.675 11.469 -2.513 0.513  -0.501 "C2'"  DL5 20 
DL5 "O2'"  "O2'"  O 0  1 N N N N N N 5.018  5.200 11.391 -3.562 0.124  0.411  "O2'"  DL5 21 
DL5 O2A    O2A    O 0  1 N N N N N N -1.477 9.003 10.239 3.448  -3.026 -1.008 O2A    DL5 22 
DL5 O2B    O2B    O 0  1 N N N N N N -4.171 6.853 11.116 6.477  0.241  -1.343 O2B    DL5 23 
DL5 C2F    C2F    C 0  1 N N N N N N 6.428  5.805 9.489  -4.450 -1.520 -1.062 C2F    DL5 24 
DL5 N2F    N2F    N 1  1 N N N N N N 5.711  5.183 8.387  -3.953 -0.972 -2.344 N2F    DL5 25 
DL5 O2F    O2F    O 0  1 N N N N N N 6.246  4.718 7.428  -4.297 0.140  -2.705 O2F    DL5 26 
DL5 O2G    O2G    O 0  1 N N N N N N -5.016 3.032 12.889 9.057  1.158  -0.168 O2G    DL5 27 
DL5 "C3'"  "C3'"  C 0  1 N N R N N N 3.505  7.148 10.880 -1.694 -0.782 -0.762 "C3'"  DL5 28 
DL5 "O3'"  "O3'"  O 0  1 N N N N N N 4.828  7.596 10.453 -2.347 -1.795 0.032  "O3'"  DL5 29 
DL5 O3A    O3A    O 0  1 N N N N N N -1.613 6.593 10.689 4.667  -0.918 -0.018 O3A    DL5 30 
DL5 C3F    C3F    C 0  1 N N N N N N 7.837  5.818 9.341  -5.593 -2.242 -1.008 C3F    DL5 31 
DL5 O3F    O3F    O -1 1 N N N N N N 4.493  5.092 8.368  -3.200 -1.632 -3.037 O3F    DL5 32 
DL5 O3G    O3G    O 0  1 N N N N N N -3.176 2.713 11.236 9.489  0.648  2.375  O3G    DL5 33 
DL5 "C4'"  "C4'"  C 0  1 N N R N N N 2.990  8.050 11.892 -0.315 -0.479 -0.138 "C4'"  DL5 34 
DL5 "O4'"  "O4'"  O 0  1 N N N N N N 2.865  7.088 13.010 -0.215 0.962  -0.139 "O4'"  DL5 35 
DL5 C4F    C4F    C 0  1 N N N N N N 8.784  6.335 10.218 -6.062 -2.760 0.199  C4F    DL5 36 
DL5 N4F    N4F    N 1  1 N N N N N N 10.115 6.328 10.039 -7.320 -3.539 0.186  N4F    DL5 37 
DL5 O4F    O4F    O -1 1 N N N N N N 10.916 6.797 10.840 -8.014 -3.743 -1.031 O4F    DL5 38 
DL5 "C5'"  "C5'"  C 0  1 N N N N N N 1.510  8.699 11.783 0.801  -1.090 -0.989 "C5'"  DL5 39 
DL5 "O5'"  "O5'"  O 0  1 N N N N N N 0.514  7.671 11.517 2.057  -0.899 -0.336 "O5'"  DL5 40 
DL5 C5F    C5F    C 0  1 N N N N N N 8.260  6.917 11.402 -5.407 -2.582 1.418  C5F    DL5 41 
DL5 O5F    O5F    O -1 1 N N N N N N 10.625 5.845 9.046  -7.829 -4.082 1.391  O5F    DL5 42 
DL5 C6F    C6F    C 0  1 N N N N N N 6.796  7.013 11.755 -4.254 -1.878 1.496  C6F    DL5 43 
DL5 N6F    N6F    N 1  1 N N N N N N 6.590  7.668 13.056 -3.560 -1.690 2.790  N6F    DL5 44 
DL5 O6F    O6F    O 0  1 N N N N N N 7.572  8.073 13.713 -2.523 -1.053 2.838  O6F    DL5 45 
DL5 O7F    O7F    O -1 1 N N N N N N 5.555  7.875 13.585 -4.026 -2.172 3.807  O7F    DL5 46 
DL5 H2     H2     H 0  1 N N N N N N 3.264  0.472 13.837 -4.893 4.699  2.476  H2     DL5 47 
DL5 HN6    HN6    H 0  1 N N N N N N -1.174 0.662 14.604 -2.426 7.320  -1.385 HN6    DL5 48 
DL5 HN6A   HN6A   H 0  0 N N N N N N -1.365 2.162 15.222 -3.605 7.997  -0.398 HN6A   DL5 49 
DL5 H8     H8     H 0  1 N N N N N N 0.327  6.352 13.370 -0.288 3.007  -1.804 H8     DL5 50 
DL5 H01    H01    H 0  1 N N N N N N -2.286 4.654 13.014 6.574  0.848  1.551  H01    DL5 51 
DL5 H01A   H01A   H 0  0 N N N N N N -3.884 5.283 13.540 6.851  -0.826 2.088  H01A   DL5 52 
DL5 "H1'"  "H1'"  H 0  1 N N N N N N 4.021  5.467 13.623 -1.659 1.341  1.324  "H1'"  DL5 53 
DL5 HO1B   HO1B   H 0  0 N N N N N N -3.345 8.249 12.633 6.794  -2.833 0.028  HO1B   DL5 54 
DL5 "H2'"  "H2'"  H 0  1 N N N N N N 2.972  5.007 10.910 -2.898 0.963  -1.417 "H2'"  DL5 55 
DL5 HO2A   HO2A   H 0  0 N N N N N N -1.417 9.421 9.388  3.340  -3.451 -0.146 HO2A   DL5 56 
DL5 HO2G   HO2G   H 0  0 N N N N N N -5.917 3.071 12.591 8.688  2.035  0.002  HO2G   DL5 57 
DL5 "H3'"  "H3'"  H 0  1 N N N N N N 2.822  7.113 10.018 -1.630 -1.038 -1.819 "H3'"  DL5 58 
DL5 H3F    H3F    H 0  1 N N N N N N 8.223  5.372 8.436  -6.152 -2.419 -1.915 H3F    DL5 59 
DL5 HO3G   HO3G   H 0  0 N N N N N N -3.372 2.600 10.313 10.444 0.784  2.309  HO3G   DL5 60 
DL5 "H4'"  "H4'"  H 0  1 N N N N N N 3.714  8.842 12.132 -0.267 -0.861 0.882  "H4'"  DL5 61 
DL5 "H5'"  "H5'"  H 0  1 N N N N N N 1.266  9.201 12.731 0.616  -2.156 -1.117 "H5'"  DL5 62 
DL5 "H5'A" "H5'A" H 0  0 N N N N N N 1.498  9.434 10.964 0.821  -0.604 -1.964 "H5'A" DL5 63 
DL5 H5F    H5F    H 0  1 N N N N N N 8.968  7.325 12.109 -5.828 -3.012 2.315  H5F    DL5 64 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
DL5 C2    N1     DOUB Y N 1  
DL5 C6    N1     SING Y N 2  
DL5 N3    C2     SING Y N 3  
DL5 C2    H2     SING N N 4  
DL5 C4    N3     DOUB Y N 5  
DL5 N9    C4     SING Y N 6  
DL5 C4    C5     SING Y N 7  
DL5 N7    C5     SING Y N 8  
DL5 C5    C6     DOUB Y N 9  
DL5 C6    N6     SING N N 10 
DL5 N6    HN6    SING N N 11 
DL5 N6    HN6A   SING N N 12 
DL5 C8    N7     DOUB Y N 13 
DL5 N9    C8     SING Y N 14 
DL5 C8    H8     SING N N 15 
DL5 "C1'" N9     SING N N 16 
DL5 O1A   PA     DOUB N N 17 
DL5 O2A   PA     SING N N 18 
DL5 PA    O3A    SING N N 19 
DL5 PA    "O5'"  SING N N 20 
DL5 O3A   PB     SING N N 21 
DL5 O2B   PB     DOUB N N 22 
DL5 PB    O1B    SING N N 23 
DL5 PB    C01    SING N N 24 
DL5 O1G   PG     DOUB N N 25 
DL5 O3G   PG     SING N N 26 
DL5 PG    C01    SING N N 27 
DL5 PG    O2G    SING N N 28 
DL5 C01   H01    SING N N 29 
DL5 C01   H01A   SING N N 30 
DL5 "C2'" "C1'"  SING N N 31 
DL5 "C1'" "O4'"  SING N N 32 
DL5 "C1'" "H1'"  SING N N 33 
DL5 O1B   HO1B   SING N N 34 
DL5 C2F   C1F    SING N N 35 
DL5 "O3'" C1F    SING N N 36 
DL5 C1F   "O2'"  SING N N 37 
DL5 C1F   C6F    SING N N 38 
DL5 "C3'" "C2'"  SING N N 39 
DL5 "O2'" "C2'"  SING N N 40 
DL5 "C2'" "H2'"  SING N N 41 
DL5 O2A   HO2A   SING N N 42 
DL5 N2F   C2F    SING N N 43 
DL5 C3F   C2F    DOUB N N 44 
DL5 O2F   N2F    DOUB N N 45 
DL5 O3F   N2F    SING N N 46 
DL5 O2G   HO2G   SING N N 47 
DL5 "O3'" "C3'"  SING N N 48 
DL5 "C3'" "C4'"  SING N N 49 
DL5 "C3'" "H3'"  SING N N 50 
DL5 C3F   C4F    SING N N 51 
DL5 C3F   H3F    SING N N 52 
DL5 O3G   HO3G   SING N N 53 
DL5 "C5'" "C4'"  SING N N 54 
DL5 "C4'" "O4'"  SING N N 55 
DL5 "C4'" "H4'"  SING N N 56 
DL5 N4F   C4F    DOUB N N 57 
DL5 C4F   C5F    SING N N 58 
DL5 O5F   N4F    SING N N 59 
DL5 N4F   O4F    SING N N 60 
DL5 "O5'" "C5'"  SING N N 61 
DL5 "C5'" "H5'"  SING N N 62 
DL5 "C5'" "H5'A" SING N N 63 
DL5 C5F   C6F    DOUB N N 64 
DL5 C5F   H5F    SING N N 65 
DL5 C6F   N6F    SING N N 66 
DL5 N6F   O7F    SING N N 67 
DL5 N6F   O6F    DOUB N N 68 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
DL5 SMILES           ACDLabs              14.52   "O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC1OC(C2OC3(OC12)C(=CC(\C=C3[N+]([O-])=O)=[N+](/[O-])[O-])[N+]([O-])=O)n1cnc2c(N)ncnc21"                                                                                                                                                    
DL5 InChI            InChI                1.06    "InChI=1S/C17H18N8O18P3/c18-14-11-15(20-4-19-14)22(5-21-11)16-13-12(8(40-16)3-39-46(37,38)43-45(35,36)6-44(32,33)34)41-17(42-13)9(24(28)29)1-7(23(26)27)2-10(17)25(30)31/h1-2,4-5,8,12-13,16H,3,6H2,(H6-,18,19,20,26,27,32,33,34,35,36,37,38)/q-1/t8-,12-,13-,16-/m1/s1" 
DL5 InChIKey         InChI                1.06    IPYWFNMUWLRGLC-KWDXPJCYSA-N                                                                                                                                                                                                                                              
DL5 SMILES_CANONICAL CACTVS               3.385   "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[C@H]4O[C]5(O[C@@H]34)C(=C[C](C=C5[N+]([O-])=O)=[N+]([O-])[O-])[N+]([O-])=O"                                                                                                                          
DL5 SMILES           CACTVS               3.385   "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH]4O[C]5(O[CH]34)C(=C[C](C=C5[N+]([O-])=O)=[N+]([O-])[O-])[N+]([O-])=O"                                                                                                                                
DL5 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+]([O-])[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"                                                                                                                               
DL5 SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+]([O-])[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"                                                                                                                                                
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
DL5 "SYSTEMATIC NAME" ACDLabs              14.52   "2',3'-O-{(1S)-2,6-dinitro-4-[oxido(oxo)-lambda~5~-azanylidene]cyclohexa-2,5-diene-1,1-diyl}-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine"                                                                                         
DL5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(6-aminopurin-9-yl)-3',5'-dinitro-6-[[oxidanyl-[oxidanyl(phosphonomethyl)phosphoryl]oxy-phosphoryl]oxymethyl]spiro[3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxole-2,4'-cyclohexa-2,5-diene]-1'-ylidene]-bis(oxidanidyl)azanium" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      DL5 
_pdbx_chem_comp_synonyms.name         TNP-AMPPCP 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DL5 "Create component"   2015-06-03 EBI  
DL5 "Other modification" 2015-09-12 EBI  
DL5 "Initial release"    2016-04-13 RCSB 
DL5 "Modify synonyms"    2021-03-01 PDBE 
DL5 "Other modification" 2026-04-05 RCSB 
# 
